loglik_bisse_shift2: BISSE loglik shift

In Giappo/sls: Likelihood model for diversification processes with single lineage rate shifts

Description

Provides BISSE loglik shift function (alternative version). Yields the old (wrong) BISSE result for the Main Clade only.

Usage

loglik_bisse_shift2(
  pars,
  brts,
  n_0 = 2,
  t_0 = 0,
  t_d,
  log_scale = TRUE,
  lambdaterms = TRUE
)

Arguments

pars	parameters of the likelihood functions: pars[1] is lambda_m, i.e. speciation rate of the main clade; pars[2] is mu_m, i.e. extinction rate of the main clade; pars[3] is lambda_s, i.e. speciation rate of the sub clade; pars[4] is mu_s, i.e. extinction rate of the sub clade;
brts	branching times provided as a list of vectors, one for the main clade, one for the subclade
n_0	starting number of lineages
t_0	starting time
t_d	decoupling time
log_scale	set it to TRUE if you desire the output in log form
lambdaterms	set it to TRUE if you desire the powers of lambda in the likelihood

Value

loglik

Author(s)

Giovanni Laudanno

Giappo/sls documentation built on Feb. 1, 2021, 9:55 a.m.